Goodbye
by Terreis
Summary: Spoilers for Season 2 premiere. What led Jemma to make her decision? Just a little introspective look. Will most likely be non-canon within a few episodes.
1. Chapter 1

A/N: I thought up this particular story after watching the season premiere. I was trying to imagine what could possibly lead Jemma to decide leaving Fitz was a good idea. I came up with this and I hope you enjoy it. Text in italics is a flashback.

Disclaimer: I don't own anything Marvel. Although I would not be averse to a Coulson action figure.

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><p>Jemma had waited nearly a solid month to see Coulson after making her decision. It hadn't been easy, keeping it a secret from everyone. She knew she had been acting somewhat oddly. Fortunately, they all chalked it up to the ongoing stress of working with Fitz, trying to help him without actually making him feel helpless.<p>

Coulson had been gone a little longer than usual this time around. Not even May knew where. The new Director of S.H.I.E.L.D. clearly felt it was better that way, although the new team leader clearly disagreed. Jemma understood May's frustration. Although Coulson had always been above them in rank, so to speak, they had all eventually formed a team.

Now everything was splintered. Ward was imprisoned, of course. Other than Fitz, Skye was the only one who hadn't seen their former teammate since coming to The Playground. Jemma had gone down once. The day Fitz regained consciousness. Ward had still been incapable of speaking and apparently past the point of trying to hide his own emotions. There was a hint of relief in his eyes when she told him Fitz would live, but Jemma refused to pay attention to it. She had begun to tell him of the damage Fitz had sustained, how the Scot's brilliant mind may never recover and it quickly dissolved into ten solid minutes of screaming at Ward.

May had eventually shown up and taken her out of the room. The next day, she found herself in a hand-to-hand combat training session with both May and Skye. Although Jemma was reluctant to do such a thing, May merely pointed out that sometimes it was better to focus anger than to bottle it up.

While the base of operations for the new S.H.I.E.L.D. was The Playground, Director Coulson was rarely there for more than a few days at a stretch. And when he was on site, there was a distance between himself and the others that hadn't existed since the very early days of the team. Skye, past her initial rage at Ward, tended to lock part of herself away these days. So Jemma felt a little distant even from the woman she considered her best friend.

Trip remained the same for the most part, although he was a little more guarded. The only person Jemma felt the least bit closer to was May. The same event that had erected some walls around other members of the team seemed to have put cracks in the walls May already had. She was quicker to smile at Jemma, quicker to give praise. Perhaps something in her felt she had to be the one to boost morale now that Coulson's own burden was so much heavier.

And Fitz. Fitz was the reason she was currently making her way to Coulson's quarters at the moment. With every step she took, her mind screamed at her to go back. It wasn't too late. No one knew what she was about to do and no one ever had to know.

But Jemma's heart was too heavy. Fitz's outburst a little over a month ago had been the final straw. He had, understandably, been short-tempered since regaining consciousness. The entire team gave him their full support and, physically, his recovery had been swift. Fitz's mental processes, however, were far below what he had always been accustomed to.

At first it hadn't been too bad. With the team cheering him on in their own ways, he remained optimistic during the first couple of weeks. His first day back in the lab had brought an abrupt end to his patience, though. Names of instruments he could handle in his sleep escaped him. As his frustration grew, so did his tendency to be snappish. They all got the sharp end of his tongue at one time or another and all of them understood the reasons and waved it away.

For Jemma, who was with him the most, it had been a roller coaster. She had grown so accustomed to the two of them finishing each other's sentences that it took her by surprise when he yelled at her one day for doing just that.

"I'm not a bloody idiot, Simmons. I can finish my own sentences!"

She had stammered out an apology which Fitz accepted silently. But she had been unable to stop herself from doing the same thing just an hour later and was stunned when his response was a smile.

It went on like that for two months. Back and forth, up and down, some days were better than others. Sometimes the bad days just kept coming with seemingly no end in sight. Those were the times when Jemma found comfort in her training sessions with May and Skye. If the other women noticed she pushed herself a little harder on those days, they never mentioned it.

Through it all, Jemma had to tell herself to be patient. Fitz WAS getting better. It was a very slow process and she did realize that his mind may not work at the same exact level it used to. But she saw small signs of improvement almost every day. She just wished Fitz could realize it as well. So a month ago, when he grew frustrated with an experiment he was trying to put together, Jemma tried to offer words of hope.

"_You need to be patient with yourself, Fitz," she told him softly, coming up behind him and laying a hand on his shoulder in a comforting gesture. "You're almost there."_

_He rounded on her so quickly that Jemma actually took a couple of steps back._

"_Patient?" he ground out. "It's been months, Jemma! And all you can tell me is to be patient?! Do you have any idea what this is like for me? Any idea at all? No, of course you don't. Why didn't you listen to me? Why did you have to save me?! You should've just let me drown!"_

_Silence rang through the air as Jemma_ _processed what she was hearing. The tears that she usually managed to hide until she was alone in her quarters sprang to her eyes._

"_Fitz…Fitz, you can't mean that."_

"_I would rather be dead than have to be dealing with this right now, Jemma."_

_He turned away from her with that pronouncement and Jemma could only stand there in stunned silence. She wanted to shake him, to scream at him, to hug him close to her and beg him not to think in such a way. She wanted to do all those things, but she felt as though she was frozen to the spot. And then it got worse._

"_I never wanted to be on a field team," he said quietly, his back still to her. "I never wanted this."_

_He had given voice to Jemma's own darkest thoughts. She was the reason they joined Coulson's team. He only came because she wanted to. Because he loved her. Yet another fact that she had yet to deal with head on simply because there was just too much else for her to shoulder at the moment._

_She had dragged him into all of this. And now he was permanently injured in the worst way possible for Fitz. Had he lost the ability to walk or even lost sensation from the neck down, Jemma was certain he would've struggled through recovery and eventually come out on top. Possibly even making jokes about his wheelchair and having Jemma help him engineer tools to assist him with his work. But it was his mind. His beautiful, glorious mind. And she had destroyed it._

"_I'm sorry," she whispered. _

_Jemma wasn't even sure he heard her. She didn't wait to find out. When she left the lab, she went straight to her quarters and didn't emerge until nearly noon the next day with her mind set on a course of action. _

_She had to leave the team._

Fitz had apologized profusely the next day, something that was rather rare these days. She had accepted it and they slipped into something of a normal pattern. Bad days were still an occurrence, but never to the extent of that particular episode. Jemma told no one of the outburst. It wouldn't do anyone any good.

Since the rescue, she had always blamed herself for Fitz being in the position of getting hurt simply because it had been her idea to join a field team. It was a feeling of guilt she tried to keep locked away because she knew it wouldn't help Fitz get better if he thought she felt responsible. The revelation that part of him blamed her, too, was just too much. If he blamed her, then perhaps her presence was a reminder of why he had to go through this. Perhaps, if she was gone, his recovery might be easier.

The weeks she had to wait between making her decision and actually speaking to Coulson had done nothing to weaken her resolve. So when she finally found herself standing in front of his door, Jemma knocked firmly and entered with her head held high when he gave her permission to come in.

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><p>AN: There will be more coming. Hopefully this evening before the second episode premieres. I live for reviews, so please feel free!


	2. Chapter 2

A/N: Point of view change in this chapter. This'll be from Coulson's point of view.

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><p>When Jemma walked into the room, Coulson could tell by the set of her shoulders that she had come to some sort of decision about something. He could tell by the look in her eyes, however, that it wasn't a decision he was going to like.<p>

"Agent Simmons," he greeted, at the same time hating himself for being so formal. But he really felt it was a necessary distance to maintain as Director.

Sometimes, he wished he could punch Fury square in the face.

"Director Coulson," she responded. "I know you're very busy. Thank you for seeing me so quickly."

Her message had been the first he received upon his return to The Playground this morning and it contained an air of something akin to desperation. He had been incredibly concerned when he first got it and had spent the last two hours going back through everyone's reports to see if anyone mentioned any incidents out of the ordinary regarding Simmons. There was nothing to be found.

"No need to thank me," he gestured for her to have a seat and he did the same. "I'd be lying right now if I said I wasn't a little concerned, though. Has something gone wrong with Fitz? Is his recovery stagnating?"

When he was gone, Skye sent him abbreviated versions of reports in short, untraceable data bursts. Nothing in any of them had alarmed him in regards to Fitz. And he had been unable to find anything in the full reports upon his return. The slight and sudden tension in Jemma's posture at the mention of the name, however, told him that something was going on.

"Not exactly, sir."

Coulson narrowed his eyes slightly at her answer. She looked down and away from him, the first time she had broken eye contact since entering the room. And in the seconds before she spoke again, Coulson felt his heart begin to sink. As if he knew what she was about to say.

"Fitz's recovery is going as well as can be expected, sir. Although it is hard for him to accept, that is the truth. I think, however, that he would be better off without certain distractions. That is to say…I think it would be best if I left The Playground."

So there it was. Her eyes met his own again and he knew in that moment he wouldn't be able to dissuade her from this course of action. He had seen that look before. On a video feed in the moments before she jumped from the plane. Jemma Simmons had made up her mind. But something in him had to try.

"Are you sure that's for the best?" he inquired softly. "You're his best friend, Simmons. He leans on you more than anyone else on this team."

Although that might be part of the problem, he suddenly realized.

"I think it is for the best. I believe I might be something of a reminder to him of how things used to be. A reminder that's too painful. And perhaps, if he wasn't always looking at his past, he might be able to concentrate more on his future."

What a lovely phrased and poetic lie. Because she was lying. He could see that straight away. Jemma had never been a good liar unless she had some elaborate backstory prepared. Coulson actually had to bite back a smile as a memory of train travel and prostitutes rose up in his mind.

She was lying and he should call her out on it. He should demand the truth from her, especially regarding such a huge decision. But he was still looking her straight in the eyes and he saw pain in them. Tremendous pain that she was actually doing a fairly good job of hiding. If it wasn't for years of experience in reading people, Coulson doubted he would see it.

He wanted to help her, to reassure her that things would eventually work out and that she didn't have to do this. He knew better than to try. It was clear to him that she hadn't talked to anyone about this. Not even Skye. And if she was willing to accept help, willing to share her burden with anyone else, she would've done it by now.

Whatever she was dealing with regarding Fitz, she was determined that she was going to do it on her own. That much was abundantly clear. Coulson found that he didn't have the heart to press her on the matter.

"I see," he spoke the words in a thoughtful tone and noted that Jemma now narrowed her own eyes. She was wondering if he knew she was lying. "Did you have any ideas on where you might go?"

"I suppose home is out of the question," she attempted a smile. "Even if I stay with my cousin in London?"

"Yes, I'm afraid home is out of the question," Coulson informed her apologetically. He wished she could go home. She had strong ties to her family, one of the few agents remaining who did. It had been against his better judgment to allow her to contact her parents at all after arriving at The Playground, but he did allow it. Once. After Skye had assured him the brief conversation would be completely secure.

No, home was not an option for Jemma. It was too dangerous. Hydra, as far as he knew, still thought both Fitz and Simmons were dead. But they were too recognizable, too well-known. All it would take was one member of Hydra to spot Jemma in a pub or in the market and everything would come crashing down around her. There would be no one to protect her at home. She could be killed. She could be captured and tortured for information. Coulson couldn't stand the thought of it.

Agent Blake, still recovering from his own run-in with Deathlok and still very loyal to S.H.I.E.L.D., had his own covert team in another facility about two thousand miles from The Playground. Jemma would be a welcome addition there. But he didn't know how comfortable she would be answering to the man who once delivered the order to have her killed. Oh, she would understand. Blake had simply been doing his job. He was one to follow the rule book, as Coulson had once been. But Coulson didn't want her to be uncomfortable.

There were precious few facilities she could go to. Blake's was the nearest. The rest were scattered across the globe. All other teams he had managed to cobble together were basically nomadic. Sleeping and eating wherever and whenever they could. Scraping by with a minimum of complaint. They were good agents, but Jemma's talents would be wasted with them.

One solution presented itself to him and he was fairly unsure of it, but it seemed better than any other alternative. Appearances could be altered somewhat. Hair dye, colored contacts, things of that sort. And even if she was discovered, she would certainly be protected.

"How would you feel about working for Tony Stark?" he asked.

The widening of her eyes indicated that his suggestion wasn't a possibility she had considered. He continued.

"We could get word to Hill somehow. She's not an agent anymore, but I know she'll help. She and Pepper could get you an alias and we'll make some small changes to your appearance. What do you think?"

She sat there for a moment, clearly taking a moment to ponder what he was proposing. Coulson was confident she would be safe there. Hill could handle almost any threat there was. Failing that, she had a direct line to Iron Man should a situation arise that was somehow beyond her. And wherever Jemma stayed was certain to be top of the line in terms of security.

When she still hadn't answered, Coulson kept talking.

"Hill knows you, knows what you are capable of. She can easily find a job for you in one of Stark's labs," he detected a flicker of interest in Jemma's eyes. "Now, I'll leave the decision of whether or not to tell Stark you're a former agent up to you. The man can keep a secret. Although he's not so keen on doing the secret identity thing, I suppose."

Jemma started to nod slowly and then stood up, prompting Coulson to do the same.

"I think that might be just the right thing, sir," she admitted. "Thank you. Any thoughts on when I might be able to leave?"

She was more eager than he thought. Again he wondered what had occurred to bring her to this point. And again he didn't push.

"Let me speak to May and Skye. We'll contact Hill, let her know you're coming. And then I'll figure out a safe way to get you there without calling too much attention."

May's team was still too hot after their last foray above ground to risk going to Stark Headquarters. The various individual agents and other teams were pretty far from The Playground to get back in any decent amount of time. He needed someone who could fly under the radar and protect Jemma adequately. An individual would be preferable and he had an idea who he could get. Not a S.H.I.E.L.D. agent, but Coulson trusted him. He couldn't say that about many people these days.

"Within the week, I think? Before I have to leave again," he decided.

Her expression softened slightly as she regarded him.

"You need to get some rest, sir. You're pushing yourself too hard."

"No need to worry about me, Simmons. I'll be fine," he tried to brush off her concern as they made their way to the door. He reached for the handle to open it for her and she startled him by putting her hand on top of his.

"Please, sir. Promise me you'll take care of yourself."

She was worried about him. Something serious had been eating away at her for weeks and she was worried about him. How typically Jemma. Coulson acknowledged in that moment just how much he would miss her. Throwing caution to the wind, he wrapped both arms around her and pulled her in for a hug. She returned the sentiment without any hesitation.

"I wish you would stay, Jemma," he said without pulling away.

Jemma trembled slightly and Coulson knew she was trying not to cry. The waver in her voice when she replied confirmed his suspicions.

"I wish I could, sir. I truly do."

They remained in their embrace for a moment, knowing this was the only informal goodbye they would get. When they pulled away, they were Agent Simmons and Director Coulson once more.

"I'll…I'll go tell Skye. She should be the first to know I'm leaving, I think. I'll tell Fitz once we've decided on a day."

"If you think that's best," Coulson told her as he began to open the door. "I'll leave it up to your discretion."

"Thank you, sir."

She walked out and turned back to him just outside the doorway.

"Shall I send May up to see you, sir?"

Translation: Could you be the one to tell May? Coulson nodded. He was of the opinion that he should probably be the one to tell May at any rate.

"Yes. Please send her up before you go see Skye. And we'll let you know as soon as we have a firm date in mind."

Jemma merely nodded in response and left. Coulson stood there for a while with the door open, listening to her retreating footsteps. When he could no longer hear her, he shut the door and sank into his chair with a sigh. He couldn't help but think that he was quite possibly the worst director in the history of S.H.I.E.L.D. at this point. If he couldn't even keep his flagship team together, how in the world was he supposed to rebuild an entire organization?


	3. Chapter 3

A/N: Conversations between Skye and Simmons, Coulson and May in this chapter. Halfway through the story, folks. Possibly a little more than halfway.

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><p>"You can't be serious."<p>

That was pretty much the reaction Jemma had expected. She took some small comfort in that fact. At least not everything was completely different.

"I am, Skye. I'm sorry. I just really think it's best for Fitz if I'm not here. Maybe…maybe I can come back at some point. I don't know. But I think I'm more of a hindrance to him than anything else."

"I don't believe this!" Skye exclaimed. Jemma gestured for her to lower her voice. The last thing she needed was Fitz overhearing them. She was pretty confident he was still in the lab, but it was better to be cautious.

"I said it might not be for good," she assured Skye. While she and Coulson hadn't discussed that explicitly, she knew he would welcome her back given the opportunity.

The question was whether the opportunity would ever present itself.

"You're running away," her friend declared, never one to hide her opinions on things. Less inclined to do so now than before Ward's betrayal.

"I am not!" it was Jemma who raised her voice now.

"You are. You're running away from Fitz and everything he's dealing with. You can't bear to watch it anymore and, Jemma, I don't blame you. I know it's hard for you. But he needs you here. You can't just abandon him."

A streak of white-hot fury coursed through Jemma and she advanced on her friend.

"I'm not abandoning him, Skye! I didn't abandon him when we were trapped and I'm not abandoning him now. He doesn't want me here. He doesn't want me around. I'm the reason he is broken. My idea to save him from drowning in the ocean. My idea to join a field team. I blame myself for what's happened to him and the only thing that's worse is that he blames me, too. Fitz blames me for everything and it's like a knife through my heart. I can't…I can't be here, Skye. I just can't do it anymore."

For the second time in the last half hour, Jemma was pulled into a tight hug. This time, she wasn't able to hold back the tears and she could just barely hear Skye making soothing noises as she tried to at least keep from outright sobbing. When Jemma had gained some semblance of control, Skye pulled away slightly although she kept one arm around her. Jemma was grateful for the closeness. It brought her some comfort.

"Did he tell you this in one of his outbursts, Jemma? You know he doesn't mean what he says when he's like that. Doesn't really help my urge to go punch him in the mouth for saying it, but he didn't mean it. I know he didn't."

"If you're planning to convince me to stay with that argument, you might as well give up," Jemma smiled a little, though there was no real humor behind it. "I've tried to tell myself that hundreds of times. But I never can believe it in this case. No, there was some truth to his words. Just enough for me to feel the sting. I really do think he'd be better off without me. At least for a while."

Skye simply stared at her for a while and Jemma could almost hear her friend's thoughts. She was trying to come up with an argument that would get Jemma to stay. Grasping at anything that might convince her she was making a mistake.

"Skye. I need to go," Jemma said softly.

It really was useless for Skye to argue with her and she saw the moment that realization hit Skye. Which was fortunate since it gave her the split second she needed to brace herself for yet another fierce hug.

"I will miss you so much," Skye whispered in her ear. Pulling back, she grabbed Jemma by the shoulders and shook her just a little. "Don't you dare think you can leave and not contact us. I'll find a safe way for all of us to communicate. You might be leaving The Playground, but you're still part of our team."

"Yes, ma'am," Jemma smiled through her own tears and was rewarded with a hug. Again.

Skye was, quite simply, a very affectionate person when her guard was down.

"Any idea when or where you're going?" Skye asked her once the hugging had come to an end.

Jemma hesitated just for a minute. Coulson hadn't said it was a secret. If they couldn't trust the remainder of their team by now…

"No idea when, yet," she responded. "I believe he and May will be trying to get me to Agent Hill. Well…former Agent Hill."

"Stark Industries?" Skye's eyebrows climbed into her hairline. "Swanky. Take lots of pictures for me. And I want Iron Man's autograph."

She was hiding behind her façade again, putting on a brave face for the time being. Jemma was grateful for the gesture.

"I'll see what I can do," she managed a tiny laugh. Difficult to do when one didn't really feel like laughing.

"And when will you tell Fitz?"

"When we have a set date," Jemma replied. "Director Coulson is hoping it will be within the next week."

"So soon…" Skye's voice was quiet. Very quiet.

"Soon is probably best. Don't you think?"

The women stared at each other in silence for a while. Skye was quite clearly not in agreement with Jemma, but she was at least recognizing that it would do no good to argue. In the end, she elected not to answer the question.

"I'm hungry," Skye announced quite suddenly. "Let's go raid the kitchens. I think Trip is hiding some cake in there somewhere."

"I'm in," Jemma agreed.

As they made their way to the kitchen, Jemma reflected that having Skye for a friend was quite possibly the best thing to happen to her in a long while. For the first time since making her decision, she allowed herself to hope that she wouldn't be gone forever.

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"You couldn't dissuade her?"

"May, there is not one person on this entire team who can easily be swayed once they've made their mind up about something. I don't want her to go. But I think, for her sake, she needs to."

May eyed him questioningly. She was taking the news of Jemma's departure about as well as Coulson had expected. The few minutes between Jemma leaving his office and May arriving had given him the chance to reflect a little on things, though.

"She is on the edge, May. Being with Fitz all the time, being his strongest avenue of support, it's wearing away at her. Mentally, emotionally, physically. You can't tell me you haven't noticed her weight loss."

It was slight, but it was there. Jemma was in fine shape to begin with. There was no need for weight loss and Coulson felt it was more than just the training sessions she'd embarked upon.

"Yes, I've noticed," May confirmed. "I just don't want to lose her. But I don't want her unhappy, either. Fitz had to have done something to trigger this. Done something, said something. You know he's always had something of a short temper depending on circumstances, but his condition has made it worse. He can be outright cruel sometimes. I've just never heard him be that way to her."

"He's frustrated with his progress and I can understand that. I wish things were different, May. I don't know that she truly wants to go, but I think she feels like she has to. If nothing else, it will let her escape for a bit. What better place for a scientist than Stark Industries?"

She fixed him with a slight glare.

"You think Tony Stark can be trusted?"

"I trust Tony Stark to look after Pepper first and foremost. And Pepper brings all her little ducklings along with her. Jemma would be among them. Do you trust Hill?"

"With my life."

A vote of confidence indeed.

"Then it's settled. We'll contact Hill and make the necessary arrangements to get Jemma to her."

"Who's the escort?" May inquired.

"Oh, I've got someone in mind," Coulson smiled slightly.

It only took a few moments for May to realize what he was planning. Really, she did scare him sometimes. He was glad she was on their side.

"He's not even an agent, Coulson."

"Director Coulson," he corrected her.

This time, the glare was much more piercing.

"That was the worst joke you've ever cracked," she informed him. "I'm going to do you a favor and pretend I didn't hear it. Now back to the main point. We're still a little uncertain as to who we can trust in regards to some of the agents we've kept. The only one who even knows our precise location is Blake. And you're going to trust an outsider with Jemma's safety?"

"I trust him precisely because he's an outsider. He's never had any affiliation with S.H.I.E.L.D. other than the very few times he's assisted me. And he saved my life, May. Yes, I trust him with Jemma's safety."

He was dead-on serious. Nothing less than absolute sincerity would convince May of the total trust he had in Spencer. She stared him down for a minute or two before finally nodding her agreement.

"Alright, then. Let's find Skye. The sooner we contact Hill the better, I suppose."

Coulson caught her hand as she walked by and turned her back towards him.

"If I thought there was a chance I could convince her to stay, Melinda, I'd still be arguing with her."

His hand was squeezed just slightly in response.

"I know you would, Phil. I know you would."

They let go of each other's hand after only a moment.

"Well, then. Let's find Skye," Coulson echoed May's earlier suggestion.

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><p>AN: I'm unable to finish this story before the second episode comes on. I apologize for that, but I will be finishing up soon. Please leave a review if you are at all inclined to do so. I'd love to know how I'm doing.


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